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REVIEW: Fragmentomics of Natural Peptide Structures

A. A. Zamyatnin1,2

1Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia; fax: (495) 954-2732; E-mail: aaz@inbi.ras.ru

2Universidad Técnica Federico Santa Maria, Departamento de Informática, El Centro Científico Tecnólogico de Valparaíso, Ave. España 1680, Valparaiso, Chile; fax: (5632) 279-75113; E-mail: alexander.zamyatnin@usm.cl

Received January 26, 2009; Revision received June 9, 2009
Natural fragmentation of peptide and other chemical structures is well known. They are a significant object of biochemical investigations. In this connection, the bases and determination are given for the notion of the “fragmentome” as a set of all fragments of a single substance, as well as for global fragmentome of all chemical components of living organisms. It is described how protein-peptide fragments are formed in nature, what experimental and theoretical methods are used for their investigation, as well as mathematical characteristics of fragmentomes. Individual fragmentomes of all subunits and of complete casein fragmentome are considered in detail. Structural and functional variety of its possible fragments was revealed by computer analysis. Formation in an organism of an exogenous–endogenous pool of oligopeptides and correlation of these data with concepts of structure–functional continuum of regulatory molecules is shown on an example of food protein fragments. Possible practical importance of the use of natural fragments in dietology, therapy, as well as in sanitary hygiene and cosmetics is noted.
KEY WORDS: fragmentomics, oligopeptide, protein, casein, structure, function, EROP-Moscow Database

DOI: 10.1134/S0006297909130100